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Rev Chgset Date Author Log Message
(edit) @3632 [3632] 7 months dk Added neighborhood-based HGT conjugation.
(edit) @3631 [3631] 7 months blwalker Hey, check it out, I fail at not deleting random sections of code. Fixed …
(edit) @3630 [3630] 7 months blwalker Fixed some comments. Clearly copy-paste had been abused…
(edit) @3629 [3629] 7 months dk Added hgt conjugation, refactored genome splitting.
(edit) @3626 [3626] 7 months blwalker Moved lineage label to the last column of SaveStructuredPopulation? so it …
(edit) @3625 [3625] 7 months blwalker I ran the long tests and didn't even notice I'd broken this one. …
(edit) @3623 [3623] 7 months blwalker Added "lineage" option to DETAIL documentation (the option was already …
(edit) @3622 [3622] 7 months dk Added HGT source option.
(edit) @3618 [3618] 7 months beckma24 Rework of active messages. Active messages no longer casue interrupts. …
(edit) @3614 [3614] 7 months connel42 Fixed logic error in my MeanKill? event
(edit) @3613 [3613] 8 months covertar Short and long consitency tests for: MIGRATION_RATE -- random migration …
(edit) @3611 [3611] 8 months covertar Added consistency test for replace deleterious.
(edit) @3606 [3606] 8 months baerb Finished first draft of the Text-View Documentation
(edit) @3604 [3604] 8 months baerb Update of the text viewer documentation. Corrected errors in the text, …
(edit) @3600 [3600] 8 months baerb Started translating the text view manual from Chri Adami's Alife to …
(edit) @3594 [3594] 8 months beckma24 Enhanced interrupt.dat
(edit) @3590 [3590] 8 months beckma24 Push data of message being sent into organism's output buffer so that …
(edit) @3589 [3589] 8 months beckma24 Sending a message is an output, so call to DoOutput? method has be …
(edit) @3587 [3587] 8 months blwalker Make destroy instruction actually destroy resources.
(edit) @3582 [3582] 8 months beckma24 Added a few more message types, 6 total. Fixed …
(edit) @3581 [3581] 8 months beckma24 Active messages can now trigger thread-based interrupts. Interrupts …
(edit) @3580 [3580] 8 months beckma24 Added instructions and config options for thread-centric version of the …
(edit) @3578 [3578] 9 months jbarrick New BASE_MERIT_METHOD 7 = assign merit from gestation time. Fixed …
(edit) @3577 [3577] 9 months beckma24 Added cHardwareCPU::InterruptThread? that is called to start an interrupt.
(edit) @3576 [3576] 9 months beckma24 Initial step toward incorporating active messages and interrupts. Added …
(edit) @3573 [3573] 9 months connel42 Changed some stats associated to organism kill events. Removed …
(edit) @3569 [3569] 9 months goingssh Added reaction requesite for total number of reactions completed (max and …
(edit) @3565 [3565] 9 months connel42 Added additional kill event that looks at the mean resource levels
(edit) @3563 [3563] 9 months brysonda Add new tBufferedList class to the tools. This class functions similar …
(edit) @3556 [3556] 9 months dk HGT refactoring.
(edit) @3553 [3553] 9 months beckma24 Added event KillWithinRadiusBelowResourceThresholdTestAll?
(edit) @3549 [3549] 9 months brysonda Add 'die' instruction to cHardwareExperimental.
(edit) @3548 [3548] 9 months brysonda Implement out and zero register instruction in cHardwareExperimental
(edit) @3547 [3547] 9 months connel42 Added additional output to orgs_killed data file and expanded kill event …
(edit) @3546 [3546] 9 months dk hgt updates. modularized fragment selection, added unbiased substring …
(edit) @3543 [3543] 9 months dk Added tracking of the beginning of an HGT match.
(edit) @3532 [3532] 10 months baerb Made changes to allow code to compile under Windows Visual Studio 2005
(edit) @3531 [3531] 10 months brysonda Tweak cHardwareExperimental goto instruction to use direct labels.
(edit) @3530 [3530] 10 months baerb Added some modification to the enzyme reaction.
(edit) @3525 [3525] 10 months brysonda Fix typos in cHardwareExperimental.
(edit) @3522 [3522] 10 months baerb Fixed typo, mainly wanted to trigger the buildbot
(edit) @3521 [3521] 10 months blwalker Change a -1 to ~0 in cBitArray; the Intel compiler was complaining about …
(edit) @3516 [3516] 10 months brysonda Update cHardwareExperimental for phase 2 tests. New/Renamed …
(edit) @3506 [3506] 11 months dk bugfix in hgt code.
(edit) @3505 [3505] 11 months brysonda Add new bgs_dyn_mutrates expected results.
(edit) @3504 [3504] 11 months brysonda Remove affected bgs_dyn_mutrates expected results
(edit) @3503 [3503] 11 months brysonda Implement a new cRunningStats class that calculates running statistics …
(edit) @3501 [3501] 11 months brysonda Fix a couple of compile warnings. Unused variable in …
(edit) @3500 [3500] 11 months blwalker New expected results for analyze_printphenotypes.
(edit) @3499 [3499] 11 months blwalker New version of CommandPrintPhenotypes?: - handles any number of tasks …
(edit) @3498 [3498] 11 months brysonda Fix infinite loop in cHardwareExperimental::FindNopSequenceStart?
(edit) @3497 [3497] 11 months blwalker Added the actual detail file which is supposed to be analyzed, whoops. …
(edit) @3496 [3496] 11 months blwalker Returning analyze_printphenotypes to using "classic" vs. "heads" …
(edit) @3495 [3495] 11 months dk updated HGT to respect genome circularity
(edit) @3494 [3494] 11 months blwalker Further fixing of analyze_printphenotypes test.
(edit) @3493 [3493] 11 months blwalker Updating analyze_printphenotypes consistency test to use new "heads" names …
(edit) @3492 [3492] 11 months brysonda And yet a few more sign-comparison warnings when built via cmake (on …
(edit) @3490 [3490] 11 months brysonda Attempt to squash one last sign-comparison warning when built via cmake.
(edit) @3489 [3489] 11 months brysonda Small fix to malloc_extension.cc. Rodan's version of linux apparently …
(edit) @3488 [3488] 11 months brysonda Merge branches/tcmalloc-1.4 into development
(edit) @3469 [3469] 11 months dk Added HGT replace option.
(edit) @3468 [3468] 11 months brysonda Add command line option to toggle configuration 'defaulting to' warnings. …
(edit) @3467 [3467] 11 months dk Added config option to override calculated deme fitnesses for competition, …
(edit) @3466 [3466] 11 months brysonda Fix some debug mode sign comparison warnings in tcmalloc.
(edit) @3465 [3465] 11 months brysonda Add state grid instructions to cHardwareExperimental.
(edit) @3464 [3464] 11 months dk Updates to HGT code, including substring matching for genomes.
(edit) @3459 [3459] 11 months connel42 Updated a few kill actions to include new stats
(edit) @3458 [3458] 11 months brysonda Squash all remaining compiler warnings under Xcode/GCC 4.2, including the …
(edit) @3457 [3457] 11 months brysonda Fix NULL instruction index in cHardwareExperimental.
(edit) @3456 [3456] 11 months beckma24 Added column to orgs_killed.dat that displayed number of unoccupied cells …
(edit) @3455 [3455] 11 months connel42 re-implemented action to kill organisms within a certain radius if some …
(edit) @3453 [3453] 11 months brysonda Cleanup cHardwareExperimental instruction variants.
(edit) @3452 [3452] 11 months dk Updated docstring for WORLD_GEOMETRY.
(edit) @3450 [3450] 11 months brysonda Correct cHardwareCPU instruction incorrectly marked as 'default'
(edit) @3448 [3448] 11 months connel42 Fixed some bugs in my print actions, added a few bitstring operators
(edit) @3447 [3447] 11 months dk Added sanity checking to flash instruction to prevent memory explosion, …
(edit) @3446 [3446] 11 months brysonda Add large population performance/consistency test.
(edit) @3445 [3445] 11 months brysonda Add support for LONG string loading and manipulation. - Eliminated the use …
(edit) @3444 [3444] 11 months brysonda Correct PrintGenotypeColorGrid? so that it performs the same coloring …
(edit) @3443 [3443] 11 months dk Added support for DEMES_PREVENT_STERILE to CompeteDemes?.
(edit) @3442 [3442] 11 months dk Added buffer size limit for opinion-setting, removed stale messaging …
(edit) @3439 [3439] 11 months brysonda Add new print action, DumpGenotypeColorGrid?. This action dumps a …
(edit) @3438 [3438] 11 months dk Refactored message-related code in cOrganism. Fixed a potential dangling …
(edit) @3437 [3437] 11 months goingssh fixed bugs in 2 new events from last commit
(edit) @3436 [3436] 11 months goingssh Added 2 new events 1. PrintNewTasksDataPlus? - prints same info as …
(edit) @3435 [3435] 11 months dk bugfix to message stat tracking when organisms are in the test CPU.
(edit) @3434 [3434] 11 months brysonda Some tweaks and corrections to 'direct' label instruction variants. These …
(edit) @3433 [3433] 11 months brysonda The Great Configuration Update of 2009! - Renamed 'classic' organisms and …
(edit) @3432 [3432] 11 months dk merging deme tournaments, generic opinion-related deme actions.
(edit) @3431 [3431] 11 months brysonda Implement concurrent support for un'label'd nop sequence instructions in …
(edit) @3430 [3430] 11 months dk merging data distribution actions, etc.
(edit) @3429 [3429] 11 months dk added missing include for algorithm.
(edit) @3428 [3428] 11 months dk Merged last remaining bits of consensus-related code.
(edit) @3427 [3427] 12 months brysonda Add simple consistency test to verify proper reaction counts for multiple …
(edit) @3426 [3426] 12 months brysonda Fix cEnvironment::TestOuput? to properly mark reactions in reaction_count …
(edit) @3425 [3425] 12 months brysonda Update Deployment-Universal target to the Mac OS X 10.5 SDK.
(edit) @3424 [3424] 12 months brysonda Alter icc settings to explicitly use ieee floating point.
(edit) @3423 [3423] 12 months brysonda Remove -ffast-math compiler argument. This should eliminate test …
(edit) @3422 [3422] 12 months brysonda Some reorganization of cDoubleSum, for clarity.
(edit) @3421 [3421] 12 months brysonda Alter stats.dat generation to avoid negative zeros (-0). This should …
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